Appendix D. Homeworks
23
Assignment 2: Introduction to the Insight II Modeling Package
and the PDB File Structure and Retrieval
1. Introduction to Insight II. If you are not familiar with Insight II you might
start by reading the short manual and the tutorial from the web site of the
home page of Molecular Simulations (MSI)
(www.accelrys.com/insight/index.html). The site URLs may change.
The manual also contains a short list of basic UNIX commands and a description of simple text editors. Some of the displays on our computers are
slightly different from those described in the tutorial but the differences
are not critical. For example, in our version the help window automatically
follows the tasks invoked from the pulldown menus, and the dial boxes
are located on the left, rather than the right, side of the screen. For more
information, refer to the Insight II User Guide.
Note: after opening Insight II, ignore the message about detection of the
unlicensed mode. Our site does not have license for the Sketch module.
Repeated warning messages might occur during the “build in” Insight II
Pilot tutorial.
2. Running Insight II. Before starting Insight II, you must define the set of
environmental variables by running two commands:
source /local/msi/cshrc
Alternately, you can insert these lines into your .cshrc file and they will
be executed by the system automatically every time you log on. In that case,
you will only need to specify the command
source .cshrc
after editing your .cshrc file the first time. When this insertion is complete, you can run Insight II by specifying the command
insightII
at the UNIX prompt. Remember, UNIX commands are case sensitive.
Note: NYU staff may have already inserted these commands in your
.cshrc file.
3. PDB Structures. Check the PDB web site for information about the type
of stored 3D structures (i.e., proteins, DNA, RNA, DNA/protein complexes,
etc.) and the amount in each group. Report your findings.
4. Retrieval of PDB Files. Using the web PDB browser, find coordinate
files for the crystal forms II and III of Bovine Pancreatic Trypsin Inhibitor
(BPTI) among the many BPTI entries. From the PDB Home page, go to
Searching and Browsing PDB and then choose PDB’s web Browser.
You can search by specifying the abbreviation “BPTI” in the Compound
window. When the search is completed, records containing BPTI (including its mutated forms) will be displayed at the bottom of the page. Note
their ID codes (a number followed by three letters). The two middle letters in this code constitute the name of the subdirectory where the file of
24
Appendix D. Homeworks
interest resides. For example, the subdirectory name for ID code 1abb is
ab and the file name pdb1abb.ent . Ftp to ftp.rcsb.org and login as
anonymous (the password instructions will be on the screen). Change directory to pub/pdb/data/structures/divided/pdb/ab and get the
desired file with the command
get pdb1abb.ent.Z
5. Format of PDB Files. Read the text in the top of both PDB files and
describe the differences in the number of recorded residues, structure resolution, number of solvent molecules, experimental conditions, etc.
Attach to the assignment sheet a printout of a few lines, starting with the
word ATOM, from a PDB file; mark with arrows and describe the content of each specific format field. (The PDB browser contains information
about the format; see also the original paper on PDB files: J. Mol. Biol.
112, 535–542, 1977).
6. Displaying a Protein in Insight II. Retrieve from PDB the file of mutated form of BPTI (ID = 7pti), and start Insight II. From the top menu
bar select Molecule 2 and then choose Get. Press the PDB button in Get
File Type and the User button specify the directory. Select the file of the
7pti structure. (Do not press Heteroatom button). Execute. The structure
of BPTI should now be on the screen. Use Object /DepthCue and then
Transform /Clip for viewing the protein.
Change the display ( Molecule /Display) to Backbone only to speed up
the response time. Label the mutated residues ( Molecule /Label).
Repeat the operations described above to display the structure of BPTI’s
crystal form II (keep both structures on the screen).
Now, overlay both structures by selecting Overlay from Transform . In
few paragraphs describe the structural differences between both forms of
BPTI.
7. Ramachandran Plots. To create a file listing with all the dihedral angles
and for a protein, you can use Protein /List from the Biopolymer
module. Select Dihedrals and the protein (any of the structures). Press
List to file button, specify the file name, and execute. From the recorded
data create a scatter plot (phase diagram), so that each point corresponds to
one ( , ) value.
2 The
following notation will be used throughout the homework assignments:
Pulldown corresponds to a menu bar pulldown.
Command corresponds to a command from the pulldown menu.
Option corresponds to an option in the dialog box of a given command.
Appendix D. Homeworks
25
Summary of Items to Hand in:
(a) Data with the amount of PDB 3D structures for each category of
biomolecules.
(b) Description of the differences in the informational part of the PDB
files for form II and form III of BPTI.
(c) Explanation of the PDB format for storing atomic coordinates.
(d) Description of the structural differences between BPTI (form II) and
the mutated form (7pti).
(e) The table with dihedral angles and listed for BPTI.
(f) Scatter plot with points ( , ) for each residue of BPTI.
Background Reading from Coursepack (Appendix B)
M. Levitt and A. Warshel, “Computer Simulation of Protein Folding”,
Nature 253, 694–698 (1975).
M. Karplus and J. A. McCammon, “The Dynamics of Proteins”, Sci. Amer.
254, 42–51 (1986).
Y. Duan and P. A. Kollman, “Pathways to a Protein Folding Intermediate
Observed in a 1-Microsecond Simulation in Aqueous Solution”, Science
282, 740–744 (1998).
H. J. C. Berendsen, “A Glimpse of the Holy Grail”, Science 282, 642–643
(1998).
X. Daura, B. Juan, D. Seebach, W. F. Van Gunsteren, and A. Mark, “Reversible Peptide Folding in Solution by Molecular Dynamics Simulation”,
J. Mol. Biol. 280, 925–932 (1998).